The two-dimensional quadrupole ion trap mass analyzer (also referred to as the linear ion trap) is well known in the mass spectrometry art, and has become a valuable and widely-used tool for the analysis of a variety of compounds. Generally described, a two-dimensional ion trap consists of a set of four elongated electrodes to which a radio-frequency (RF) trapping voltage is applied in a prescribed phase relationship to radially confine ions to the trap interior. Axial confinement of the ions may be effected by application of a suitable direct current (DC) offset to end sections of the rod electrodes and/or electrodes located longitudinally outward of the rod electrodes. The mass spectrum of the trapped ions may be acquired by mass-sequentially ejecting the ions from the trap interior to an associated detector, either in a radial direction orthogonal to the central longitudinal axis of the ion trap, as described in U.S. Pat. No. 5,420,425 to Bier et al., or in an axial direction parallel to the central longitudinal axis, as described in U.S. Pat. No. 6,177,668 to Hager. The enlarged ion volume, greater trapping capacity, and higher trapping efficiency of the two-dimensional ion trap offers significant performance advantages (relative to the conventional three-dimensional ion trap), including enhanced sensitivity and the ability to perform an increased number of multiple stages of ion selection and fragmentation.
Successful operation of an ion trap mass analyzer requires the addition of a buffer gas (typically helium) to the trap interior. The buffer gas (also variously referred to in the art as damping or collision gas) serves two primary purposes. First, the buffer gas reduces the ions' kinetic energy via collisions. This reduction of kinetic energy is essential, not only for trapping ions injected into the trap, but also for kinetically cooling (damping) and spatially (both axially and radially) concentrating the ion cloud before mass analysis, resulting in useful mass spectral resolution and sensitivity. Second, the presence of the buffer gas enables efficient fragmentation of ions via collision activated dissociation (CAD) for tandem mass spectrometry (MS/MS or MSn) analysis.
It is known, however, that collisions of ions with buffer gas during the ion isolation and mass-sequential ejection processes may be detrimental to mass spectral performance, both by reducing resolution and by contributing to chemical mass shifts that limit mass accuracy. Instrument designers have attempted to reduce these detrimental effects by selecting a buffer gas pressure (typically between 1-5 milliTorr) that provides adequate trapping/cooling and fragmentation action while minimizing the adverse influence on resolution and mass accuracy. While this “compromise pressure” approach has resulted in generally satisfactory instrument performance, there has been recent interest in modes of operation that favor lower pressures. It is known that higher resolution may be achieved by resonantly ejecting ions at values of the Mathieu parameter q which are somewhat lower than the stability limit value of 0.908. This gain in resolution may also be traded for more rapid scan rates, i.e., mass spectra having resolution equivalent to that obtained using standard techniques may be acquired more rapidly, thereby increasing sample throughput and/or increasing the numbers of MSn cycles that can be completed. Furthermore, ejection at reduced values of q offers other advantages, including expanded mass range scanning and the possibility of employing higher order resonances to increase ejection rates and/or provide higher mass-to-charge ratio (m/z) resolution. It is noted that the problem of chemically dependent mass shifts, which may increase significantly with lowered q ejection values in certain ion traps and under certain conditions, may present a potential obstacle to the use of reduced-q resonant ejection. Chemically dependent mass shift can be lessened by reducing the buffer gas pressure, but doing so has a substantial adverse effect on the ability to trap and cool ions, and to efficiently fragment ions via the CAD mechanism.
U.S. Pat. No. 6,960,762 to Kawato et al., while not specifically addressing reduced-q resonant ejection, describes an adaptation to a conventional three-dimensional ion trap that is designed to avoid the disadvantages arising from the presence of a buffer gas. In the Kawato et al. apparatus, the buffer gas is controllably added (via a pulsed valve) to the ion trap interior to raise the pressure to a value optimized for ion capture. After ions have been injected into the trap, the flow of the inert gas is reduced or terminated and the ion trap interior pressure is consequently lowered to a value optimized for the mass-sequential scan. By switching between the two pressures, the Kawato et al. apparatus purportedly achieves both excellent capture efficiency and scan resolution. However, the time needed to repeatedly change and stabilize the ion trap pressure may significantly lengthen the overall mass analysis cycle time and reduce sample throughput, particularly where high-capacity ion traps are employed.
At least one prior art reference discloses a dual-trap mass spectrometer architecture in which pressures in the traps are separately optimized for different functions. Zerega et al. (“A Dual Quadrupole Ion Trap Mass Spectrometer”, Int. J. Mass Spectrometry 190/191 (1999) 59-68) describes a dual ion trap mass spectrometer consisting of a first three-dimensional quadrupole ion trap (referred to as the “preparation cell”) operated at a pressure of approximately 10−4 Torr, which is coupled to a second three-dimensional quadrupole ion trap (referred to as the “mass analysis cell”) operated at a pressure of about 10−7 Torr. In this mass spectrometer, ions are internally generated within the preparation cell and cooled by collisions with inert gas atoms to reduce the volume occupied by the ion cloud. The ions are then ejected from the preparation cell (by turning off the confinement voltage and applying suitable DC voltages to the end caps) through a small aperture in one of the end caps and travel to the mass analysis cell, where they are admitted into the cell's interior volume through an inlet aperture. The mass-to-charge ratios of the ions trapped in the mass analysis cell are determined by a complex technique based on measurement of the secular frequencies of the trapped ions via trajectory analysis, in which ions are confined within the trap for a prescribed period and then ejected (through an exit aperture) to a detector for generation of an ion signal representative of the ions' time-of-flight between the trap interior and the detector. This technique requires analysis of the ion signal as a function of confinement time, so several mass analysis cycles must be performed to obtain a complete mass spectrum. The complexity of the mass analysis technique disclosed in the Zerega et al. paper, as well as the need to execute several mass analysis cycles to generate a mass spectrum, disfavor commercial use of this apparatus.